GBuilder - An application for the visualization and integration of EST cluster data

This paper presents a network-centric DNA sequence visualization and analys is tool called GBuilder. The tool is an easy-to-use Java application that c an be used to analyze DNA sequence clusters and assemblies. The emphasis is on the analysis of EST data, where these highly redundant collections of l ow-quality and often alternatively spliced or chimeric sequence data are di fficult to explore. The tool has the capacity to visualize similarities or dissimilarities between sequences at the level of the nucleotide base or an notation in many ways. Sequences may also be edited manually. The novel fea ture of GBuilder is its ability to access different data sources and analys is applications available on the Internet and to integrate these results an d functionality back into itself. External resources such as EST cluster da tabases and conventional command-line analysis applications are integrated and accessed using CORBA (Common Object Request Broker Architecture), which provides a standard implementation independent protocol for integration. N ew CORBA services can be integrated immediately if they use a known interfa ce described using the Interface Definition Language.